#118 bsub runCA

Feature (48)

I'm trying to want to do some distributed computation with runCA using bsub on a LSF.
Has anyone tried it, or documented bsub commands corresponding to qsub commands?

Magdalena Zarowiecki
Wellcome Trust Sanger Institute


  • Jason Miller

    Jason Miller - 2010-01-25
    • assigned_to: nobody --> jasonmiller9704
  • Jason Miller

    Jason Miller - 2010-01-25

    We don't run the LSF grid job control engine. Do you know SGE and LSF? If so, then we would be much obliged if you could help us enhance our grid support by porting our SGE commands to LSF. Maybe you could explore the issue and report back. For starters, you could identify yourself by logging in to Source Forge and submitting a new feature request. (This request is attributed to Nobody because the submitter wasn't logged in.) Then, consider that we use three SGE features. (1) submit a job (2) submit a series of jobs (3) submit a job but don't run until after this other job finishes. What are the equivalent LSF commands? To get more specifics, you can issue runCA with "useGrid=1 scriptOnGrid=0". The runCA exec will print out 'qsub' commands to submit the parallel pieces. Perhaps you can convert those to LSF commands. In the end, if indeed there are one-for-one counterparts in LSF for all our SGE comands, we'll be happy to offer a 'runCA -LSF' option. -- Jason Miller

  • Sergey Koren

    Sergey Koren - 2015-01-14

    CA 8.2 has support for LSF with the gridEngine=LSF option. All the sge* options should also be updated to their LSF equivalents to request resources.

  • Sergey Koren

    Sergey Koren - 2015-01-14
    • status: open --> closed

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